On a hillside in Cuyamaca Rancho State Park, charred pine snags stood like big, blackened toothpicks, remnants of the 2003 Cedar Fire. Surrounding them, scrubby patches of ceanothus, or mountain lilac, sprouted up from seeds kindled by the flames.

It’s the kind of regrowth you might expect the year following a major wildfire. But this was a decade after the Cedar Fire burned through 273,246 acres of San Diego County, scorching 95 percent of the park and destroying 98 percent of its mature conifer trees. To date, little of the forest has returned.

The blaze, which started ten years ago this month, was the largest forest fire in California history, based on fire perimeter maps used to document burned areas since the early 1900’s, according to state park documents. And it burned with catastrophic intensity, taking 15 lives and 2,232 homes, and searing oak and conifer woodlands down to bare mineral soil.

While a natural fire burn would follow a patchwork pattern, leaving some acreage with little damage, the Cedar Fire leveled nearly everything.

“In comparison to a more natural burn this was the result of seven or eight decades of fire suppression,” said Mike Puzzo, an environmental scientist with the park. “When it got into the understory, there was no stopping it.”

It’s the result of fire fighting policies that left Western forests in a state of “fire deficit,” said Stephen Fillmore , forest fuels officer for the Cleveland National Forest.

“What happened in the conifer systems (during the Cedar Fire) is very similar to what’s happening around the west in conifer ecosystems. “We’ve gone out and done the Smoky the Bear thing and put every fire out, for the sake of the timber, for the sake of aesthetics.”

That allows the growth of unnaturally dense forests, with thick understory of what fire fighters call “ladder fuels.”

“When you have a fire come through, it allows fire to extend into the canopies and takes the whole forest at once,” Fillmore said.

The Cedar Fire and subsequent burns in 2007 wiped out more than half of the mixed conifer in San Diego County, according to park documents. Cuyamaca saw the worst of it. Before the fire, conifers covered about 40 percent of the park, in pine-oak woodlands and mixed conifer forest, Puzzo said. All but a few stands were incinerated.

A decade later, the alien terrain left after the blaze is recovering to varying degrees. In some spots, such as Fern Flat, charred stumps are surrounded by what Puzzo called a “monoculture” of ceanothus.

In nearby West Mesa, where the fire burned less intensely, signs are more encouraging. Scrub and saplings mingle with 15 to 20 foot oak trees which shot up since the fire. Several miles away, in a meadow near Los Vaqueros, some large pines survived, and new ones are cropping up.

“I think this place is recovering very nicely,” Puzzo said. “This right here is a good representation of what a fire should do. Some is dead, but a lot is still alive.”

At neighboring William Heise County Park, only a couple hundred of the park’s nearly thousand acres burned, said Supervising Park Ranger Roger Covalt. Gnarled oak snags cover some of its hillsides, but a few, whose roots survived the blaze, are springing back to life and sprouting new branches from their stumps.

“You’ll see these dead oaks, but you’ll see life coming out of it,” Covalt said. “It’s Mother Nature coming back.”

Countywide, however, some of the creatures that inhabited the burn zone aren’t returning, said Robert Fisher, a herpetologist with the U.S. Geological Survey.

Fisher and his colleagues had been sampling 55 plots at four locations in San Diego County, near La Jolla, Otay Mountain, Jamul and Santa Ysabel, as part of the San Diego Multiple Species Conservation Program, which sets aside land for wildlife protection. Those surveys allowed them to compare how the creatures fared after the fire.

What they found was that some species of small mammals and reptiles that prefer open habitat thrived after the fires. Others, including moisture-loving salamanders, snakes and shrews vanished from fire-scorched scrubland.

That led researchers to question whether the severity of the fire exceeded the creatures’ ability to bounce back. Scientists had assumed that the animals, which evolved to tolerate fire, would rebound quickly.

“In reality, what we’re seeing is that some of these animals aren’t recovering,” Fisher said. “That’s creating concern on our part about the resiliency of the landscape.”

While crews have rushed to stamp out forest fires, chaparral has burned too often, said Alexandra Syphard, a senior research scientist with the Conservation Biology Institute. Repeated burns can stunt the recovery of natural shrub land and allow exotic grasses to take over, she said.

Scientists have also discovered that fire-scarred areas of chaparral aren’t protected from subsequent blazes. Various researchers estimate that between 20,000 to 60,000 acres of shrub land affected by the Cedar fire re-burned in 2007.

“One really important lesson to learn is that different vegetation types and different ecological areas are adapted to different fire regimens,” Syphard said. “At any point those natural variations in the fire regimen are disrupted, it can be highly destructive to the natural system.”

Animation depicts spread of Cedar Fire

Animation shows spread of 2003 Cedar Fire. Created by Harry D. Johnson, Department of Geography, San Diego State University.

How to restore those natural systems is a point of debate.

Ceanothus, a chaparral species with vivid blue and purple flowers, is one of the first plants to crop up after a fire. It’s a California native, and fixes nitrogen in the soil. But it’s so ubiquitous that scientists disagree on whether it’s paving the way for forest recovery, or crowding out other plants.

In Cuyamaca, where ceanothus dominates the landscape, crews are burning back the bushes to replant pines, Puzzo said. But on the Cleveland National Forest, they’re leaving it alone, said deputy fire management officer Brian Rhodes.

Reforestation efforts have had mixed results. Forest service crews replanted about 10 acres on Laguna Mountain, Rhodes said. The saplings withered in the following drought, he said, but made a tasty meal for deer that flourished after the fire.

“We didn’t have very good success,” Rhodes acknowledged, but added that other conifer seedlings sprouted spontaneously.

In Cuyamaca, crews are replanting 2,530 acres – about a tenth of the park. That’s a small portion of the former forest, but they hope it will be the starting point for recovery. Nonetheless, the ecological aftermath of the Cedar Fire may not be known for a century.

“If we’re successful with the reforestation project, an area like this hill will have mature Coulter and Jeffrey pines, and their seeds will eventually disperse,” said Puzzo, who started his career at the park in 2004, the year after the fire. “But I will have been long retired when that question is answered.”